I generally use a home made phenol:Chloroform extraction protocol (Employing SDS and glass beads for cell lysis). This gives loads and loads of DNA, then I clean the DNA up with a commercial spin column. This has been used successfully for Archea (Sulfolobus), Bacteria (E. coli), Yeast (S. cerevisiae) and Cyanobacteria (too many to list).

In my experience commercial kits aren`t vigorase enough when it comes to cell lysis (esp for cyano DNA extraction, they have a thick peptidoglycan cell wall).

Sonication will also work, using a probe that actually goes into the cell paste works best but a sonication water bath should also induce cell lysis (remember to put ice in it though to keep the temp down).

[quote="genetim"]Can boiling break the cell wall and the cell membrane of the bacteria?[/quote]

I imagine it probably does, but i think you need to get the correct timing. A 10 minute boil PCRed a dream for me. Use about a 1ul suspension, if your supernatant is yellowish then it probably contains proteins as you used too heavy an innoculation. Boiling for too long will probably degrade the DNA. 10 minutes should be fine for 1ml PBS.

This is a home made recipe:Prepare this Lysis buffer (Chip Lysis Buffer):

50 mM Tris, pH around 8.0 10 mM EDTA 1% SDS

Then mix these:50% of Phenol(pH around 7.8 )/Chloroform 25% of Lysis buffer (Chip Lysis Buffer)25% of Water

Now you can use it for DNA extraction:Add 1 ml of that mixture above with pellet of bacteria or cells.Dissolve bacteria or cells by pipetting up and down.Keep vials on ice for 10 min.put vials on vortexer horizontally and vortex for 15 seconds.Centrifuge >11000 g for 15 minTake supernatant.Add the same volume of Isopropanol and invert several times and stay for 10 min at RT.Centrifuge again. and wash pellet with 70-75 % Ethanol.